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Merge pull request #420 from massimoaria/develop
issue #404: OpenAlex integration
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| utils::globalVariables(c("all_of", "corr", "DI", "id_oa","RP","UN","AU_ID")) | ||
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| csvOA2df <- function(file){ | ||
| options(readr.num_columns = 0) | ||
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| ## import all files in a single data frame | ||
| for (i in 1:length(file)){ | ||
| #D <- read.csv(file[i], quote='"', check.names = F, stringsAsFactors = F) #fileEncoding = "UTF-8-BOM") | ||
| D <- read_csv(file[i], na=character(), quote='"', trim_ws = FALSE, progress = show_progress(), show_col_types = FALSE) %>% | ||
| mutate(across(where(is.numeric), as.character)) %>% | ||
| mutate(across(where(is.character), \(x) tidyr::replace_na(x,""))) %>% | ||
| as.data.frame() | ||
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|
||
| if (i>1){ | ||
| l <- intersect(l,names(D)) | ||
| DATA <- rbind(DATA[l],D[l]) | ||
| }else{ | ||
| l <- names(D) | ||
| DATA <- D} | ||
| } | ||
| rm(D) | ||
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| ## Post-Processing | ||
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| # column re-labelling | ||
| DATA <- relabelling(DATA) | ||
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| # recode as numeric | ||
| DATA$TC <- as.numeric(DATA$TC) | ||
| DATA$PY <- as.numeric(DATA$PY) | ||
| DATA$relevance_score <- as.numeric(DATA$relevance_score) | ||
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| # replace | with ; | ||
| DATA <- DATA %>% | ||
| mutate(across(where(is.character), ~ stringi::stri_replace_all_regex(.,"\\|",";"))) | ||
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| DATA$AF <- DATA$AU | ||
| DATA$ID <- DATA$DE | ||
| DATA$AB="" | ||
| DATA$CR <- gsub("https://openalex.org/","",DATA$CR) | ||
| DATA$AU_ID <- gsub("https://openalex.org/","",DATA$AU_ID) | ||
| DATA$id_oa <- gsub("https://openalex.org/","",DATA$id_oa) | ||
| DATA$JI <- DATA$J9 <- gsub("https://openalex.org/","",DATA$SO_ID) | ||
| DATA$corresponding_author_ids <- gsub("https://openalex.org/","",DATA$corresponding_author_ids) | ||
| DATA$C1 <- gsub("https://", "", DATA$C1) | ||
| DATA$DB <- "OPENALEX" | ||
|
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| ## corresponding author | ||
| UN <- strsplit(DATA$C1,";") | ||
| corresp <- strsplit(DATA$authorships_is_corresponding,";") | ||
| df_UN <- data.frame(UN=unlist(UN), id_oa=rep(DATA$id_oa,lengths(UN))) %>% | ||
| group_by(id_oa) %>% | ||
| mutate(n=row_number()) | ||
| df_COR <- data.frame(corr=unlist(corresp), id_oa=rep(DATA$id_oa,lengths(corresp))) %>% | ||
| group_by(id_oa) %>% | ||
| mutate(n=row_number()) | ||
| df_UN <- df_UN %>% | ||
| left_join(df_COR, by=(c("id_oa","n"))) | ||
| AU <- strsplit(DATA$AU,";") | ||
| AU_df <- data.frame(RP = unlist(AU), AU_ID=unlist(strsplit(DATA$AU_ID,";")), id_oa=rep(DATA$id_oa,lengths(AU))) %>% | ||
| group_by(id_oa) %>% | ||
| mutate(n=row_number()) %>% | ||
| left_join(df_UN %>% select("UN","id_oa", "corr", "n"), | ||
| by = c("id_oa","n")) %>% | ||
| dplyr::filter(corr == "true") %>% | ||
| mutate(RP = paste(RP,UN, sep=", ")) %>% | ||
| ungroup() %>% | ||
| select("RP", "AU_ID") %>% | ||
| distinct(AU_ID, .keep_all = TRUE) | ||
| DATA <- DATA %>% | ||
| left_join(AU_df, by = c("corresponding_author_ids" = "AU_ID")) | ||
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|
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| # move all char strings to Upper | ||
| ind <- apply(DATA,2,function(x){ | ||
| sum(regexpr("https://",x)>-1, na.rm = TRUE)>0 | ||
| }) | ||
| label <- names(ind)[ind==FALSE & !is.na(ind)] | ||
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| DATA <- DATA %>% | ||
| mutate(across(all_of(label), toupper), | ||
| DI = gsub("https://doi.org/","",DI), | ||
| DI = ifelse(DI == "null",NA,DI)) | ||
|
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| return(DATA) | ||
| } | ||
|
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| relabelling <- function(DATA){ | ||
| ## column re-labelling | ||
| label <- names(DATA) | ||
| label[label %in% "id"] <- "id_oa" | ||
| label[label %in% "display_name"] <- "TI" | ||
| label[label %in% "primary_location_display_name"] <- "SO" | ||
| label[label %in% "primary_location_id"] <- "SO_ID" | ||
| label[label %in% "primary_location_host_organization"] <- "PU" | ||
| label[label %in% "primary_location_issns"] <- "ISSN" | ||
| label[label %in% "primary_location_issn_l"] <- "ISSN_I" | ||
| label[label %in% "primary_location_landing_page_url"] <- "URL" | ||
| label[label %in% "primary_location_pdf_url"] <- "URL_PDF" | ||
| label[label %in% "author_ids"] <- "AU_ID" | ||
| label[label %in% "author_names"] <- "AU" | ||
| label[label %in% "author_orcids"] <- "OI" | ||
| label[label %in% "author_institution_names"] <- "C3" | ||
| label[label %in% "cited_by_count"] <- "TC" | ||
| label[label %in% "publication_year"] <- "PY" | ||
| label[label %in% "type"] <- "DT" | ||
| label[label %in% "biblio_issue"] <- "IS" | ||
| label[label %in% "biblio_volume"] <- "VL" | ||
| label[label %in% "referenced_works" ] <- "CR" | ||
| label[label %in% "keywords_keyword"] <- "DE" | ||
| label[label %in% "concepts_display_name"] <- "CONCEPTS" | ||
| label[label %in% "topics_display_name"] <- "TOPICS" | ||
| label[label %in% "sustainable_development_goals_display_name"] <- "SDG" | ||
| label[label %in% "primary_topic_field_display_name"] <- "SC" | ||
| label[label %in% "mesh_descriptor_name"] <- "MESH" | ||
| label[label %in% "referenced_works_count"] <- "NR" | ||
| label[label %in% "language"] <- "LA" | ||
| label[label %in% "authorships_author_position"] <- "AU_POSITION" | ||
| label[label %in% "authorships_raw_affiliation_string"] <- "C1" | ||
| label[label %in% "doi"] <- "DI" | ||
| names(DATA) <- label | ||
| return(DATA) | ||
| } |
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